The Types of Probiotics, Explained by a Clinician

There are hundreds of probiotic species and strains, which can make choosing one feel much more complicated than it needs to be.

Clinically, I find it much more useful to organize probiotics into three broad categories:

1. Lactobacillus and Bifidobacterium blends
2. Saccharomyces boulardii
3. Soil-based, or Bacillus, probiotics

Each category contains different microorganisms and has slightly different strengths. Understanding these three groups can make it much easier to decide which probiotic makes the most sense for you.

Let’s look at how they differ, what the research tells us about each, and whether you really need all three.

Types of Probiotics: The Three Main Categories Explained

Probiotics can be described at several levels: type (genus), species, and strain. For example, Lactobacillus is a genus, Lactobacillus rhamnosus is a species, and an individual strain (e.g., Lactobacillus rhamnosus GG) is a more specific version within that species. For practical use, I also group probiotics into broader categories or types based on the kinds of microorganisms they contain.

Other probiotic types exist beyond these three, including Streptococcus, Enterococcus, and newer organisms like Akkermansia muciniphila. Research on these is still developing, and they aren’t yet part of standard clinical use the way the three categories below are. For most people, these three categories cover what the evidence supports and what we use in practice.

You’ll often see a lot of emphasis placed on choosing a specific probiotic strain for a specific symptom. I believe that level of strain specificity is overstated and can make probiotic selection unnecessarily complicated. Clinically, I find it more useful to focus on probiotic categories and species, because the evidence tends to show overlap in benefits within these groups.

Type 1: Lactobacillus and Bifidobacterium Probiotics

What it is: Lactobacillus and Bifidobacterium probiotics are the most widely studied category of probiotics and the type most people are familiar with, often seen in probiotic foods like yogurt.

These products usually combine several species from the Lactobacillus and Bifidobacterium families. Lactobacillus species are typically found throughout the digestive tract, while Bifidobacterium species are more commonly concentrated in the large intestine.

What it does: These probiotics generally do not permanently colonize the gut. Instead, they appear to provide benefits while they pass through, helping support the gut environment, immune function, and the balance of the microbiome.

Research on Lactobacillus and Bifidobacterium blends is especially strong for digestive symptoms. They have been studied for:

• Immunity and microbiome support 1
• Anxiety 2
• Inflammatory bowel disease (IBD) 3
• Allergic and inflammatory conditions 4
• Vaginal and urinary tract infections 5
• Bacterial overgrowth 6

Because this category has the broadest research base, it is often a practical starting point for someone who is new to probiotics or looking for general digestive support.

Common species include:

• Lactobacillus acidophilus
• Lactobacillus rhamnosus
• Lactobacillus plantarum
• Lactobacillus reuteri
• Bifidobacterium longum
• Bifidobacterium infantis
• Bifidobacterium lactis
• Bifidobacterium bifidum

Type 2: Saccharomyces boulardii

What it is: Saccharomyces boulardii, or S. boulardii, is a beneficial yeast rather than a bacterium. That makes it distinct from Lactobacillus, Bifidobacterium, and most other probiotics. Like many probiotics, S. boulardii does not permanently colonize the gut. It passes through the digestive tract while exerting its effects.

What it does: S. boulardii appears to be especially useful for supporting the gut during disruptions from antibiotics, infections, and other forms of dysbiosis. Research suggests it may help reduce diarrhea, support recovery from certain intestinal infections, and improve the balance of the gut microbiome 7 8.

S. boulardii has been used successfully in research for:

• Irritable bowel syndrome (IBS) 9
• Diarrhea 10
• C. difficile infections and related diarrhea 7 11
• Crohn’s disease 7 
• Inflammatory bowel disease 12
• Parasitic infections with Giardia 13 and Blastocystis hominis 14
• Increasing clearance of H. pylori infection 15 16

Because S. boulardii is a yeast, antibiotics that target bacteria generally do not kill it. That makes it a particularly useful probiotic to consider during or after antibiotic treatment.

Unlike the other two categories, S. boulardii isn’t a genus with multiple species. It’s a single, well-defined species, most often labeled as Saccharomyces boulardii or Saccharomyces cerevisiae var. boulardii on product labels.

Type 3: Soil-Based Probiotics

What it is: Soil-based probiotics are usually made from Bacillus species, including Bacillus coagulans and Bacillus subtilis. Unlike the other probiotic types, this category of probiotic can colonize your gut 17. They’re also called spore-forming probiotics because these bacteria can enter a dormant spore state. That spore structure makes them especially resilient. They can better withstand heat, stomach acid, and other harsh conditions as they move through the digestive tract.

What it does: A number of soil-based species show health benefits, including Bacillus coagulans and Bacillus subtilis 18. 

Research shows soil-based probiotics help:

• Improve diarrhea, abdominal pain, bloating, and stool consistency in people with IBS 19 20
• Reduce acute diarrhea 21
• Improve constipation 22 23
• Decrease leaky gut 24
• Decrease adverse events from antibiotics 25
• Decrease inflammation 18 26
• Decrease respiratory tract infections 27

Common species include:

• Bacillus clausii
• Bacillus coagulans
• Bacillus subtilis

Which Type of Probiotic Should You Take?

Each of the three probiotic categories has value on its own, and there are situations where starting with one category makes sense.

In the clinic, though, we often use all three categories together. This is the Probiotic Triple Therapy approach. The idea is simple: Lactobacillus–Bifidobacterium blends, Saccharomyces boulardii, and soil-based probiotics each bring something slightly different to the table. Combining them gives you broader probiotic coverage than relying on a single category alone.

The Triple Therapy approach also helps avoid getting overly focused on finding one “perfect” strain for one specific symptom. The three probiotic categories have overlapping benefits, and using them together may give you a more complete effect.

If you’re still unsure and would like help selecting a probiotic, take my Gut Health Quiz.

The Bottom Line

Most probiotics fall into one of three categories: Lactobacillus–Bifidobacterium blends, Saccharomyces boulardii, and soil-based probiotics. Each has its own research base and its own strengths, so the category matters more than chasing a specific strain.

If you’re new to probiotics or want general digestive support, a Lactobacillus–Bifidobacterium blend is a reasonable place to start. If you’re on antibiotics or dealing with diarrhea, Saccharomyces boulardii has the most relevant evidence. If you’ve tried a probiotic before without enough improvement, a soil-based option or a combination of categories may fill in the gap.

For more persistent symptoms, we typically use all three together, an approach we call Triple Therapy, since the categories tend to cover different parts of the picture rather than duplicating each other.

If you’re not sure where to start, you can book a consultation with our clinic if your symptoms haven’t responded to probiotics on their own.

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